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gmhhope / fall-postbacc-journal-club-2022

This is a repository to share ideas for the Fall postbacc journal club (PBJ) in 2022
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PBJ4 summary #85

Closed gmhhope closed 1 year ago

gmhhope commented 1 year ago

Harsha

78

The illustration for study designs (subfigures A) are great additions to the paper to demonstrate the timeline of the vaccination/collection stages.

Yes, this is one of the major strengths of this paper. It also demonstrates that giving reviewer easier life will help author get their papers published easier.

Tabular layouts for participant characteristics (Tables 1 & 2) for vaccinations and boosters, respectively, do not need to be included as main diagrams.

I think this is required because human T cell immunity is significantly influenced by age/gender. For example, CD4/CD8 T cells are proportionally decreased along ageing. Thus the relatively closed age/gender proportion should be explicit in the main text. Also see: https://www.science.org/doi/epdf/10.1126/sciimmunol.abj1750. Table 1.

I am finding difficulty justifying the relevancy of the memory subset flow cytometry plot in figure 3B (bottom left). How does the distinction between these memory subsets support of consolidate the flow cytometry T cell figures under DMSO and Spike stimulation conditions?

Excellent question. I have no clues as well. And their previous paper (citation 8) also did not include this memory cell panel. I also cannot find any relevant mentioning in the main text. So I will agree to remove it.

Dendritic cell and other APC activity? The non-significance of T-cell response/neutralization activity could be in part to an attenuated APC (MHC I and II) activity due to SARS-CoV-2.

This will be out of the scope but you are in the right direction. But there is one critical aspect that the peptide pools did not consider whether the mutations impact the processing of antigens in APCs. As such in vitro APC-T cell assay to allow APC naturally processing of natural form of S spike proteins and present antigens to CD4/CD8 T cells will be an ideal complementary assay.

This comparison would demonstrate severity differences across multiple viruses.

Good ideas. This is really thought for higher systematic level of understanding human Vaccinology. However, for this paper, it will be out of scope. But good that you mention it.

Could there be a similar maturation amongst T cells (Th1 and Th2) in their recognition of the spike protein?

T cells were selected in thymus but after they egress from thymus, they do not under somatic mutation to further "shuffle" their TCRs. Thus, there has no somatic mutation concept for T cell biology.

For the ChAdOx-1 S (Astrazeneca) vaccine, I do not understand why the collection at day 28 appears after the vaccination day 56 (Fig 1A); this is chronologically out of order and breaks the flow of the diagram.

This is following the obligatory schedule for vaccine treatment. I assumed that for ChAdOx-1 S, it is required to get 2nd dose after 8-weeks while for mRNA-1273 is after 4-weeks. Then, for two-dose vaccine, 4-weeks post vaccination is the time to collect the samples while for single-dose vaccine, they decide to collect it after 8 week.

Paige

79

Some people get a combination of vaccines. Like some people will get Pfizer for their first two doses and then Moderna for their boosters. I would be curious to see how those individuals stand up against those who got the same company.

They specifically tested Ad26.COV2.S/BNT162b2 & 2x mRNA-1273/BNT162b2.

Chaewon

80

How does antibody levels and T cell response vary for covid variants in regards to different immunization methods? The paper explores covid variant severity profiles and how preexisting vaccination and immunity may affect them.

Methods & Data, Authors' interpretation

Very good summary.

Could look into Novavax vaccine too

Yes, that is completely protein-based vaccine and if they have the data, it will be a great addition!

Cohort comprised of different age group - participants in the ChAdOx-1 S group were significantly older (20~30 yrs older than other group's median age). Could take a look into cohort of similar age group for future studies.

Good point!

Megan

81

Some interesting possibilities are including different geographic areas (comparing vaccinated individuals across multiple continents or in rural/suburban/urban settings), increasing the age range to include children and older adults, and including immunocompromised or unvaccinated individuals.

Great points! But probably for next papers, if they can recruit/stratify them with enough sample size. Probably one thing they should explode and provide description is medical history, because during 6 months, a lot of things may happen (for example break through infection). Those should be reported. Did they report any cases that have breakthrough infection?

I had to look up the immunological markers and their significance. I'm still a bit unclear on the significance of FSC-H and FSC-A, which supposedly mean height and area, respectively. How does what's in the chart mean "singlet" and what is the significance of singlet?

FSC-A/FSC-H can be used for mainly two folds: (1) FSC can be roughly used for cell type differentiations. For example, APCs usually will be larger then T cells and it will be clearly to be seen in FSC. (2) The more important aspect is to remove doublets and gate only on "singlet". Why? Because if you include "doublet", they might increase marker staining intensity significantly. So those cells might be false positive when you used in the later gating procedure.

What was their rationale for using Calu-3 cells?

This is an excellent question! Explanation was given in page 2 of 12: Human airway Calu-3 cells were used for virus propagation and neutralization assays because SARS-CoV-2 enters these cells using the TMPRSS2-mediated entry pathway (36–39). This entry pathway is used in vivo and prevents adaptations in S, commonly observed in Vero cells.
See more in https://pubmed.ncbi.nlm.nih.gov/34960703/

Kimberly Heath

82

The authors should next look at whether T cell protection is sufficient to confer protection from severe disease in the absence of potent neutralizing antibody response in infection of SARS-CoV-2 with Omicron variant.

Think of possibility? What aspect you want to test? Causality vs. Correlation? How your experiment can fit into an experiment or recruit a particular group of patients? It will be easy to hypothesize but it will especially important to also think about how to investigate it.

Why was there no statistical comparison between groups done? Under the statistical analysis section in the methods, the authors state "Multiple comparisons were always performed as the variants versus WT, and variants were not compared between themselves."

That is an extremely good point. Yes, that looks not appropriate! Because if two variants both significantly different compared to WT. Then, it is important to compare two variants and statistically test whether they are different significantly. They escaped problems probably because the overall trends are more obvious.

The authors give no explanation as to why one cohort's serum was collected at 56 days, instead of 28 days as the rest. There is also no explanation as to why the cohorts are so heavily skewed to male participants, or why two groups were in their 60s compared to the rest in which the ages range from 20s to 50s.

A very good point! Thanks for pointing out. Yes, that is no a single paragraph to describe their demographics, though they were presented in the table. The same thing with memory subset in Fig. 3. I guessed this was originally in the peer review or in the original version. Then they should be removed. Otherwise, it is so strange to put in the main figure without any paragraphs to discuss.

Zijian

83

increase sample size and stratify data by age/biological sex/underlying conditions to minimize confounding variables.

That is a very important pitfall for this study.

figure 4 would be more convincing if they include comparison for both homologous and heterologous boosters?

Good point! If this is going for a higher journal, this will be definitely asked. I think many results were supported by many other reports published in the earlier wave. #79

I'm confused by their blood sample collection point (ie different number of days post vaccination, especially for figure 4) and will that affect the validity of the study?

I think that is based on how many doses of vaccine you received. They rationalized probably by (1) 1-dose: 8 weeks; (2)2-dose: 4 weeks; 3-dose: 2 weeks. The rationale is more or less OK but it is also subjected for debation.

Kamari

84

The COVID-19 Omicron variant is spreading quickly even among those vaccinated. GeeurtsvanKessel and colleagues hope to asses how neutralizing antibodies and T cell responses differ between the covid-19 variants (Beta, Delta and Omicron). The authors are especially interested in how T cell immunity to the variants are impacted by mRNA vaccination. These are pressing questions needed to address the rapid spread of covid-19 variants and its implication on vaccine efficacy.

🥳 Very good! The style is almost matched completely to peer review!

gmhhope commented 1 year ago

General

CD4+ and CD8+ T cell AIM assay

Other issues: